Though I know David doesn't recommend it as ideal, I choose to the use hanging files to hold my folders up. Consistent with the recommendation for one who chooses to use the hanging files (like me), I use one hanging file for each manila folder. Keeping a pinch of empty hanging files in the front of the drawers, and a bunch more in the back, I have ready access to empty hanging files whenever I put a new folder in.
If I'm 100% sure I'm going to be taking a manila folder out for just moments, I leave the hanging file it was in right where it was. If I might be using it for long enough to need to retrieve at least one other manila folder (and/or if I know I'm going to be taking that folder with me), I take the hanging file that it was in and put it in the back or front stash of empty hanging files (depending on which side it's closer to), and simply grab an empty hanging file again when it's time to put that folder back in.
Why do I do this? I've personally found the ability to flip through the manila folders far easier when they glide easily on the hanging files. The only downside I've found is that you can't fit as many folders into a drawer as you'd be able to sans hanging files. For me, personally, this is a very acceptable trade-off for the ease of folder flipping afforded by the gliding, always-vertical hanging files.